Contacts of the helix formed by residues 439 - 448 (chain A) in PDB entry 4FYT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A SER* 4.5 7.4 - - - +
419A TYR* 2.7 38.6 + - - -
435A MET* 3.0 18.1 + - + +
438A ASN* 1.3 82.0 - - - +
440A VAL* 1.3 69.8 + - + +
441A TYR 3.5 1.1 - - - -
442A ARG 3.9 0.4 - - - -
443A VAL* 3.0 25.6 + - - +
477A TYR* 5.7 0.2 - - - +
478A SER* 3.0 40.1 + - - +
481A ALA* 4.0 16.8 - - + +
482A SER* 3.8 5.8 - - - +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A MET 3.0 16.2 + - - +
436A VAL* 3.5 15.7 - - - +
439A ASP* 1.3 74.2 - - + +
441A TYR* 1.3 67.9 + - + +
443A VAL* 3.4 3.0 - - - +
444A MET* 3.1 50.9 + - + +
482A SER* 3.4 24.0 - - - +
485A ARG* 4.4 18.4 - - - -
626A VAL* 4.1 24.9 - - + +
627A THR 6.1 0.4 - - - +
628A GLY 4.8 4.9 - - - +
629A TYR* 4.1 9.0 - - + -
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Residues in contact with TYR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A VAL* 2.9 43.0 + - + +
437A LEU* 4.5 17.5 - - + +
440A VAL* 1.3 78.2 - - + +
442A ARG* 1.3 67.9 + - - +
444A MET* 3.5 32.3 + - + +
445A ALA* 3.7 9.7 + - - +
626A VAL* 3.6 16.5 - - + +
630A TYR 5.1 2.8 + - - -
631A ARG* 3.5 18.8 + - + -
659A ALA* 4.6 2.2 - - + -
660A GLN* 3.4 41.3 + - - +
663A ASN* 3.5 43.8 + - + +
664A ASP* 3.6 10.0 + - - -
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Residues in contact with ARG 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A LEU 3.5 11.9 + - - +
438A ASN* 3.2 24.5 + - - +
439A ASP 3.4 2.7 + - - +
440A VAL 3.3 0.2 - - - -
441A TYR* 1.3 80.4 - - - +
443A VAL* 1.3 60.7 + - - +
444A MET 3.5 0.2 + - - -
445A ALA* 3.6 15.2 + - - +
446A VAL* 4.5 3.1 + - - +
473A ASP 4.8 0.6 + - - -
474A ALA* 3.7 30.3 - - + +
477A TYR* 4.3 10.3 - - - +
478A SER* 2.8 30.4 + - - -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A ASP 3.0 20.9 + - - +
440A VAL 3.4 5.4 - - - +
442A ARG* 1.3 73.5 - - - +
444A MET* 1.3 68.4 + - - +
445A ALA 3.1 3.8 + - - -
446A VAL* 3.2 3.8 + - + +
447A ASP* 2.9 20.1 + - - +
474A ALA* 3.3 44.4 - - + +
475A ILE* 3.6 21.5 - - + +
478A SER* 3.8 5.4 - - - +
479A LYS* 3.7 19.7 - - + +
482A SER* 4.3 0.2 - - - +
629A TYR* 3.5 22.7 - - + +
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Residues in contact with MET 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A VAL* 3.1 34.2 + - + +
441A TYR* 3.6 28.3 - - + +
442A ARG 3.4 1.2 - - - -
443A VAL* 1.3 76.4 - - - +
445A ALA* 1.3 62.9 + - - +
448A ALA* 3.1 26.3 + - - +
549A PHE* 3.6 25.3 - - + -
629A TYR* 3.7 20.2 - - + -
630A TYR* 3.5 42.8 - - - +
631A ARG* 3.5 33.3 + - - +
667A ASN* 5.5 0.7 - - - +
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A TYR 3.7 7.2 + - - +
442A ARG 3.6 14.4 + - - +
443A VAL 3.1 0.6 - - - -
444A MET* 1.3 79.9 - - - +
446A VAL* 1.3 65.8 + - + +
448A ALA 3.7 4.3 + - - -
449A LEU* 4.0 6.2 - - - +
568A LEU* 3.7 23.2 - - + +
631A ARG* 4.9 0.8 - - - +
667A ASN* 5.3 5.6 - - - +
943A LYS* 5.9 2.1 - - - +
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Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A ARG 5.2 1.6 - - - +
443A VAL* 3.2 14.8 + - + +
445A ALA* 1.3 78.8 - - + +
447A ASP* 1.3 60.8 + - - +
448A ALA 3.1 5.4 - - - -
449A LEU* 3.2 29.9 + - + +
452A SER* 3.4 10.4 - - - +
474A ALA* 4.2 24.0 - - + -
475A ILE* 4.4 11.2 - - + -
903A GLN* 3.8 22.0 - - - +
939A GLN* 4.2 22.4 + - - +
943A LYS* 4.5 9.9 - - - +
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Residues in contact with ASP 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A VAL 2.9 13.5 + - - +
445A ALA 3.4 0.2 - - - -
446A VAL* 1.3 76.9 - - - +
448A ALA* 1.3 56.3 + - - +
449A LEU 3.3 5.9 + - - +
452A SER* 2.7 26.3 + - - -
453A HIS 4.2 0.9 - - - +
475A ILE* 3.5 17.5 - - + +
479A LYS* 3.1 21.6 + - - +
547A MET* 4.1 1.4 - - - +
548A GLY* 3.0 39.8 + - - -
549A PHE* 3.8 9.4 - - + -
565A HIS* 4.7 1.2 + - - -
566A PHE 4.6 1.6 - - - +
629A TYR* 2.8 31.5 + - - +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A MET 3.1 15.8 + - - +
446A VAL 3.1 1.6 - - - -
447A ASP* 1.3 76.8 - - - +
449A LEU* 1.3 61.6 + - - +
549A PHE* 4.1 2.2 - - + -
566A PHE* 3.6 39.0 - - + -
567A LEU* 3.4 9.2 - - - +
568A LEU* 3.0 43.0 + - + +
569A ASP 4.9 0.5 + - - -
667A ASN* 5.9 0.7 - - - +
942A GLU* 4.8 0.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il